Florence Mpaayei, now 17 and a mother of a three-year-old son, alleges that defence minister Julius Sunkuli, from her rural Narok district, raped her at his Nairobi office when she was 14.
It is the biggest sex case involving a pupil and a senior public figure in a country where sexual harassment of schoolgirls is rife. More than 15,000 girls leave primary and secondary school each year after becoming pregnant.
Mr Sunkuli will appear in court today to answer the charges, following an application by Ms Mpaayei and the Kenya Chapter of the Federation of Intenational Women Lawyers (FIDA) to have him face private prosecution.
In her affidavit presented to the court on June 9, the girl said she reported the attack to the provincial administration in Narok without success.
When government officials failed to help her she went to the attorney general's chambers who referred her to FIDA.
However, when FIDA was preparing her case, police officers took her from Nairobi to a senior chief near her home to ensure "she did not return to the city to disturb the minister", it is alleged.
Summoned with Mr Sunkuli are John Ole Rumpe, local administrator in Sunkuli's consistuency, and senior police officer Scaver Mbogho, charged with kidnap and conspiring to defeat justice.